23 results on '"Filipa, Cox"'
Search Results
2. Aspects of microbial communities in peatland carbon cycling under changing climate and land use pressures
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Clare H. Robinson, Jonathan P. Ritson, Danielle M. Alderson, Ashish A. Malik, Robert I. Griffiths, Andreas Heinemeyer, Angela V. Gallego-Sala, Anne Quillet, Bjorn J.M. Robroek, Chris Evans, Dave M. Chandler, David R. Elliott, Emma L. Shutttleworth, Erik A. Lilleskov, Ezra Kitson, Filipa Cox, Fred Worrall, Gareth D. Clay, Ian Crosher, Jennifer Pratscher, Jon Bird, Jonathan Walker, Lisa R. Belyea, Marc G. Dumont, Nichole G.A. Bell, Rebekka R.E. Artz, Richard D. Bardgett, Roxane Andersen, Simon M. Hutchinson, Susan E. Page, Tim J. Thom, William Burn, and Martin G. Evans
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archaea ,bacteria ,climate change ,fungi ,resilience ,Ecology ,QH540-549.5 - Abstract
Globally, major efforts are being made to restore peatlands to maximise their resilience to anthropogenic climate change, which puts continuous pressure on peatland ecosystems and modifies the geography of the environmental envelope that underpins peatland functioning. A probable effect of climate change is reduction in the waterlogged conditions that are key to peatland formation and continued accumulation of carbon (C) in peat. C sequestration in peatlands arises from a delicate imbalance between primary production and decomposition, and microbial processes are potentially pivotal in regulating feedbacks between environmental change and the peatland C cycle. Increased soil temperature, caused by climate warming or disturbance of the natural vegetation cover and drainage, may result in reductions of long-term C storage via changes in microbial community composition and metabolic rates. Moreover, changes in water table depth alter the redox state and hence have broad consequences for microbial functions, including effects on fungal and bacterial communities especially methanogens and methanotrophs. This article is a perspective review of the effects of climate change and ecosystem restoration on peatland microbial communities and the implications for C sequestration and climate regulation. It is authored by peatland scientists, microbial ecologists, land managers and non-governmental organisations who were attendees at a series of three workshops held at The University of Manchester (UK) in 2019–2020. Our review suggests that the increase in methane flux sometimes observed when water tables are restored is predicated on the availability of labile carbon from vegetation and the absence of alternative terminal electron acceptors. Peatland microbial communities respond relatively rapidly to shifts in vegetation induced by climate change and subsequent changes in the quantity and quality of below-ground C substrate inputs. Other consequences of climate change that affect peatland microbial communities and C cycling include alterations in snow cover and permafrost thaw. In the face of rapid climate change, restoration of a resilient microbiome is essential to sustaining the climate regulation functions of peatland systems. Technological developments enabling faster characterisation of microbial communities and functions support progress towards this goal, which will require a strongly interdisciplinary approach.
- Published
- 2023
- Full Text
- View/download PDF
3. A Previously Undescribed Helotialean Fungus That Is Superabundant in Soil Under Maritime Antarctic Higher Plants
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Kevin K. Newsham, Filipa Cox, Chester J. Sands, Mark H. Garnett, Naresh Magan, Claire A. Horrocks, Jennifer A. J. Dungait, and Clare H. Robinson
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Antarctica ,14C (or carbon-14) ,carbon ,13C ,Chalara ,Helotiales ,Microbiology ,QR1-502 - Abstract
We report a previously undescribed member of the Helotiales that is superabundant in soils at two maritime Antarctic islands under Antarctic Hairgrass (Deschampsia antarctica Desv.). High throughput sequencing showed that up to 92% of DNA reads, and 68% of RNA reads, in soils from the islands were accounted for by the fungus. Sequencing of the large subunit region of ribosomal (r)DNA places the fungus close to the Pezizellaceae, Porodiplodiaceae, and Sclerotiniaceae, with analyses of internal transcribed spacer regions of rDNA indicating that it has affinities to previously unnamed soil and root fungi from alpine, cool temperate and Low Arctic regions. The fungus was found to be most frequent in soils containing C aged to 1,000–1,200 years before present. The relative abundances of its DNA and RNA reads were positively associated with soil carbon and nitrogen concentrations and δ13C values, with the relative abundance of its DNA being negatively associated with soil pH value. An isolate of the fungus produces flask-shaped phialides with a pronounced venter bearing masses of conidia measuring 4.5–6(7) × 1.8–2.5 μm, suggestive of anamorphic Chalara. Enzymatic studies indicate that the isolate strongly synthesizes the extracellular enzyme acid phosphatase, and also exhibits alkaline phosphatase and naphthol-AS-BI-phosphohydrolase activities. Ecophysiological measurements indicate optimal hyphal growth of the isolate at a pH of 4.2–4.5 and a water potential of −0.66 MPa. The isolate is a psychrotroph, exhibiting measureable hyphal growth at −2°C, optimal hyphal extension rate at 15°C and negligible growth at 25°C. It is proposed that the rising temperatures that are predicted to occur in maritime Antarctica later this century will increase the growth rate of the fungus, with the potential loss of ancient C from soils. Analyses using the GlobalFungi Database indicate that the fungus is present in cold, acidic soils on all continents. We advocate further studies to identify whether it is superabundant in soils under D. antarctica elsewhere in maritime Antarctica, and for further isolates to be obtained so that the species can be formally described.
- Published
- 2020
- Full Text
- View/download PDF
4. Forest tree growth is linked to mycorrhizal fungal composition and function across Europe
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Mark A. Anthony, Thomas W. Crowther, Sietse van der Linde, Laura M. Suz, Martin I. Bidartondo, Filipa Cox, Marcus Schaub, Pasi Rautio, Marco Ferretti, Lars Vesterdal, Bruno De Vos, Mike Dettwiler, Nadine Eickenscheidt, Andreas Schmitz, Henning Meesenburg, Henning Andreae, Frank Jacob, Hans-Peter Dietrich, Peter Waldner, Arthur Gessler, Beat Frey, Oliver Schramm, Pim van den Bulk, Arjan Hensen, Colin Averill, and Natural Environment Research Council (NERC)
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Science & Technology ,animal structures ,Ecology ,ECTOMYCORRHIZAL FUNGI ,ACQUISITION ,05 Environmental Sciences ,DIVERSITY ,NITROGEN AVAILABILITY ,Environmental Sciences & Ecology ,REDUNDANCY ,INOCULATION ,06 Biological Sciences ,Forests ,Microbiology ,Plant Roots ,Trees ,SOIL ,10 Technology ,Mycorrhizae ,CENOCOCCUM-GEOPHILUM ,COMMUNITIES ,Life Sciences & Biomedicine ,GLOBAL BIOGEOGRAPHY ,Ecology, Evolution, Behavior and Systematics ,Ecosystem - Abstract
Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale., The ISME Journal, 16 (5), ISSN:1751-7362, ISSN:1751-7370
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- 2022
5. Multiple environmental factors influence 238U, 232Th and 226Ra bioaccumulation in arbuscular mycorrhizal-associated plants
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Jeanette Rosas-Moreno, P. R. Lythgoe, Helena S. Davies, Jon K. Pittman, Filipa Cox, Clare H. Robinson, Alastair D. Bewsher, and Francis R. Livens
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0301 basic medicine ,Environmental Engineering ,Arbuscular mycorrhizal fungi ,chemistry.chemical_element ,010501 environmental sciences ,01 natural sciences ,thorium ,Radium ,Glomeromycota ,03 medical and health sciences ,Environmental Chemistry ,Waste Management and Disposal ,0105 earth and related environmental sciences ,Abiotic component ,Rhizosphere ,Radionuclide ,Environmental radioactivity ,biology ,fungi ,Plants ,Uranium ,biology.organism_classification ,Pollution ,radium ,030104 developmental biology ,chemistry ,Bioaccumulation ,Environmental chemistry - Abstract
Ecological consequences of low-dose radioactivity from natural sources or radioactive waste are important to understand but knowledge gaps still remain. In particular, the soil transfer and bioaccumulation of radionuclides into plant roots is poorly studied. Furthermore, better knowledge of arbuscular mycorrhizal (AM) fungi association may help understand the complexities of radionuclide bioaccumulation within the rhizosphere. Plant bioaccumulation of uranium, thorium and radium was demonstrated at two field sites, where plant tissue concentrations reached up to 46.93 μg g −1 238 U, 0.67 μg g −1 232 Th and 18.27 kBq kg −1 226 Ra. High root retention of uranium was consistent in all plant species studied. In contrast, most plants showed greater bioaccumulation of thorium and radium into above-ground tissues. The influence of specific soil parameters on root radionuclide bioaccumulation was examined. Total organic carbon significantly explained the variation in root uranium concentration, while other soil factors including copper concentration, magnesium concentration and pH significantly correlated with root concentrations of uranium, radium and thorium, respectively. All four orders of Glomeromycota were associated with root samples from both sites and all plant species studied showed varying association with AM fungi, ranging from zero to >60% root colonisation by fungal arbuscules. Previous laboratory studies using single plant-fungal species association had found a positive role of AM fungi in root uranium transfer, but no significant correlation between the amount of fungal infection and root uranium content in the field samples was found here. However, there was a significant negative correlation between AM fungal infection and radium accumulation. This study is the first to examine the role of AM fungi in radionuclide soil-plant transfer at a community level within the natural environment. We conclude that biotic factors alongside various abiotic factors influence the soil-plant transfer of radionuclides and future mechanistic studies are needed to explain these interactions in more detail.
- Published
- 2018
6. Towards a microbial process-based understanding of the resilience of peatland ecosystem service provisioning – a research agenda
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Gareth Clay, Clare H. Robinson, David Elliott, Mike Longden, Erik A. Lilleskov, Richard D. Bardgett, Dave M. Chandler, Emma Shuttleworth, Tim Thom, Filipa Cox, Sarah Chadburn, James Rowson, Damian W. Rivett, Marc G. Dumont, Susan Page, Lisa R. Belyea, Angela Harris, Roxane Andersen, Angela V. Gallego-Sala, Martin Evans, Anne Quillet, William Burn, Bjorn J. M. Robroek, Simon M. Hutchinson, Andrew G. Stimson, Andreas Heinemeyer, Jonathan P. Ritson, Rebekka R. E. Artz, Jennifer Pratscher, Jonathan Walker, Nicholle G. A. Bell, Danielle Alderson, Alexandra E. Burkitt, Iain Diack, Beth Cole, Jonathan R. Lloyd, Robert I. Griffiths, Ashish A. Malik, and Catherine M. Heppell
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Environmental Engineering ,Peat ,010504 meteorology & atmospheric sciences ,Climate change ,Wetland ,010501 environmental sciences ,01 natural sciences ,Fires ,Ecosystem services ,Carbon Cycle ,Soil ,Environmental Chemistry ,Ecosystem ,Temporal scales ,Resilience (network) ,Waste Management and Disposal ,0105 earth and related environmental sciences ,geography ,geography.geographical_feature_category ,Land use ,business.industry ,Environmental resource management ,Aquatic Ecology ,Pollution ,Carbon ,Wetlands ,Environmental science ,business - Abstract
Peatlands are wetland ecosystems with great significance as natural habitats and as major global carbon stores. They have been subject to widespread exploitation and degradation with resulting losses in characteristic biota and ecosystem functions such as climate regulation. More recently, large-scale programmes have been established to restore peatland ecosystems and the various services they provide to society. Despite significant progress in peatland science and restoration practice, we lack a process-based understanding of how soil microbiota influence peatland functioning and mediate the resilience and recovery of ecosystem services, to perturbations associated with land use and climate change.\ud \ud We argue that there is a need to: in the short-term, characterise peatland microbial communities across a range of spatial and temporal scales and develop an improved understanding of the links between peatland habitat, ecological functions and microbial processes; in the medium term, define what a successfully restored ’target’ peatland microbiome looks like for key carbon cycle related ecosystem services and develop microbial-based monitoring tools for assessing restoration needs; and in the longer term, to use this knowledge to influence restoration practices and assess progress on the trajectory towards ‘intact’ peatland status.\ud \ud Rapid advances in genetic characterisation of the structure and functions of microbial communities offer the potential for transformative progress in these areas, but the scale and speed of methodological and conceptual advances in studying ecosystem functions is a challenge for peatland scientists. Advances in this area require multidisciplinary collaborations between peatland scientists, data scientists and microbiologists and ultimately, collaboration with the modelling community.\ud \ud Developing a process-based understanding of the resilience and recovery of peatlands to perturbations, such as climate extremes, fires, and drainage, will be key to meeting climate targets and delivering ecosystem services cost effectively.
- Published
- 2021
7. Ectomycorrhizal fungal composition and function predict tree growth across Europe
- Author
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Mark A. Anthony, Thomas W. Crowther, Laura M. Suz, Sietse van der Linde, Colin Averill, Marcus Schaub, Martin I. Bidartondo, Filipa Cox, Lars Vesterdal, Bruno Devos, Pasi Rautio, and Marco Ferretti
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Tree (data structure) ,Botany ,Function (mathematics) ,Biology ,Composition (combinatorics) - Abstract
Ectomycorrhizal fungi are central members of the forest fungal community, forming symbiosis with most trees in temperate and boreal forests, enhancing plant access to limiting soil nutrients. Decades of greenhouse studies have shown that specific mycorrhizal fungi enhance tree seedlings growth and nutrient uptake rates, and that these effects are sustained when seedlings are out-planted into regenerating forests. Whether these relationships scale up to affect the growth of mature trees and entire forests harboring diverse fungal communities remains unknown. In this study, we combined a continental set of European forest inventory data from the ICP forest network with molecular ectomycorrhizal fungal community surveys to identify features of the mycorrhizal mycobiome linked to forest productivity. We found that ectomycorrhizal fungal community composition was a key predictor of tree growth, and this effect was robust to statistically accounting for climate, nitrogen deposition, soil inorganic nitrogen availability, soil pH, and forest stand characteristics. Furthermore, ectomycorrhizal fungi with greater genomic investment in energy production and inorganic nitrogen metabolism, but lower investment in organic nitrogen acquisition, were linked to faster tree growth. Lastly, we sampled soils from fast and slow growing forests and introduced their microbiomes into a sterilized growth medium to experimentally isolate microbiome effects on tree development. Consistent with our observational analysis, tree seedling growth was accelerated when inoculated with microbiomes from fast vs. slow growing forests. By linking molecular community surveys and long-term forest inventory data in the field, and then pairing this with a microbiome manipulation study under controlled conditions, this work demonstrates an emerging link between the forest microbiome and dominant European tree growth rates.
- Published
- 2021
8. A previously undescribed Helotialean fungus that is superabundant in soil under maritime Antarctic higher plant
- Author
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Chester J. Sands, Clare H. Robinson, Jennifer A.J. Dungait, Kevin K. Newsham, Filipa Cox, Claire A. Horrocks, Mark H. Garnett, and Naresh Magan
- Subjects
0106 biological sciences ,Microbiology (medical) ,Hyphal growth ,Hypha ,Carbon-14 ,Deschampsia antarctica ,lcsh:QR1-502 ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,lcsh:Microbiology ,Conidium ,03 medical and health sciences ,14C (or carbon-14) ,Soil pH ,Botany ,Internal transcribed spacer ,13C ,Original Research ,030304 developmental biology ,0303 health sciences ,Chalara ,biology ,carbon ,fungi ,Helotiales ,biology.organism_classification ,Carbon ,14C ,Antarctica ,Pyrosequencing - Abstract
We report a previously undescribed member of the Helotiales that is superabundant in soils at two maritime Antarctic islands under Antarctic Hairgrass (Deschampsia antarctica Desv.). High throughput sequencing showed that up to 92% of DNA reads, and 68% of RNA reads, in soils from the islands were accounted for by the fungus. Sequencing of the large subunit region of ribosomal (r)DNA places the fungus close to the Pezizellaceae, Porodiplodiaceae, and Sclerotiniaceae, with analyses of internal transcribed spacer regions of rDNA indicating that it has affinities to previously unnamed soil and root fungi from alpine, cool temperate and Low Arctic regions. The fungus was found to be most frequent in soils containing C aged to 1,000–1,200 years before present. The relative abundances of its DNA and RNA reads were positively associated with soil carbon and nitrogen concentrations and δ13C values, with the relative abundance of its DNA being negatively associated with soil pH value. An isolate of the fungus produces flask-shaped phialides with a pronounced venter bearing masses of conidia measuring 4.5–6(7) × 1.8–2.5 μm, suggestive of anamorphic Chalara. Enzymatic studies indicate that the isolate strongly synthesizes the extracellular enzyme acid phosphatase, and also exhibits alkaline phosphatase and naphthol-AS-BI-phosphohydrolase activities. Ecophysiological measurements indicate optimal hyphal growth of the isolate at a pH of 4.2–4.5 and a water potential of −0.66 MPa. The isolate is a psychrotroph, exhibiting measureable hyphal growth at −2°C, optimal hyphal extension rate at 15°C and negligible growth at 25°C. It is proposed that the rising temperatures that are predicted to occur in maritime Antarctica later this century will increase the growth rate of the fungus, with the potential loss of ancient C from soils. Analyses using the GlobalFungi Database indicate that the fungus is present in cold, acidic soils on all continents. We advocate further studies to identify whether it is superabundant in soils under D. antarctica elsewhere in maritime Antarctica, and for further isolates to be obtained so that the species can be formally described.
- Published
- 2020
9. Organic Complexation of U(VI) in Reducing Soils at a Natural Analogue Site : Implications for Uranium Transport
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Jon K. Pittman, William R. Bower, Neil D. Gray, J. Frederick W. Mosselmans, Pieter Bots, Margaret C. Graham, Clare M. McCann, Helena S. Davies, Clare H. Robinson, Satoshi Utsunomiya, Samuel Shaw, Katherine Morris, Adam J. Fuller, Peter Leary, Francis R. Livens, Filipa Cox, Gareth T. W. Law, Michael Muir, and Department of Chemistry
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Water Pollutants, Radioactive ,Environmental Engineering ,Health, Toxicology and Mutagenesis ,0208 environmental biotechnology ,116 Chemical sciences ,chemistry.chemical_element ,02 engineering and technology ,010501 environmental sciences ,SURFACE COMPLEXATION ,SEDIMENT ,Ferric Compounds ,01 natural sciences ,Redox ,STRUCTURAL PARAMETERS ,Soil ,Uraninite ,TRACE-METALS ,Environmental Chemistry ,QD ,MONONUCLEAR U(IV) ,Groundwater ,Needle's eye ,MICROBIAL REDUCTION ,Soil Microbiology ,0105 earth and related environmental sciences ,Radionuclide ,HUMIC ACIDS ,URANYL ,Chemistry ,Soil organic matter ,Public Health, Environmental and Occupational Health ,Radioactive waste ,Biogeochemistry ,General Medicine ,General Chemistry ,Uranium ,Uranium Compounds ,Pollution ,020801 environmental engineering ,Radionuclide biogeochemistry ,Natural analogue site ,EXAFS ,X-Ray Absorption Spectroscopy ,13. Climate action ,Radioactive Waste ,Environmental chemistry ,Soil water ,MATTER - Abstract
Understanding the long-term fate, stability, and bioavailability of uranium (U) in the environment is important for the management of nuclear legacy sites and radioactive wastes. Analysis of U behavior at natural analogue sites permits evaluation of U biogeochemistry under conditions more representative of long-term equilibrium. Here, we have used bulk geochemical and microbial community analysis of soils, coupled with X-ray absorption spectroscopy and mu-focus X-ray fluorescence mapping, to gain a mechanistic understanding of the fate of U transported into an organic-rich soil from a pitchblende vein at the UK Needle's Eye Natural Analogue site. U is highly enriched in the Needle's Eye soils (similar to 1600 mg kg(-1)). We show that this enrichment is largely controlled by U(VI) complexation with soil organic matter and not U(VI) bioreduction. Instead, organic-associated U(VI) seems to remain stable under microbially-mediated Fe(III)-reducing conditions. U(IV) (as non-crystalline U(IV)) was only observed at greater depths at the site (>25 cm); the soil here was comparatively mineral-rich, organic-poor, and sulfate-reducing/methanogenic. Furthermore, nanocrystalline UO2, an alternative product of U(VI) reduction in soils, was not observed at the site, and U did not appear to be associated with Fe-bearing minerals. Organicrich soils appear to have the potential to impede U groundwater transport, irrespective of ambient redox conditions. (C) 2020 The Authors. Published by Elsevier Ltd.
- Published
- 2020
10. Predicting climate change impacts on maritime Antarctic soils: A space-for-time substitution study
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Mark H. Garnett, Claire A. Horrocks, Filipa Cox, Clare H. Robinson, Jennifer A.J. Dungait, and Kevin K. Newsham
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Deschampsia antarctica ,Soil Science ,Climate change ,Microbiology ,biomakers ,Organic matter ,Precipitation ,13C ,chemistry.chemical_classification ,δ13C ,biology ,15N ,Global warming ,04 agricultural and veterinary sciences ,biology.organism_classification ,climate change ,chemistry ,14C ,Sub- and maritime Antarctica ,Environmental chemistry ,Soil water ,040103 agronomy & agriculture ,Guano ,0401 agriculture, forestry, and fisheries ,Environmental science ,sub- and maritime Antarctica ,Biomarkers - Abstract
We report a space-for-time substitution study predicting the impacts of climate change on vegetated maritime Antarctic soils. Analyses of soils from under Deschampsia antarctica sampled from three islands along a 2,200 km climatic gradient indicated that those from sub-Antarctica had higher moisture, organic matter and carbon (C) concentrations, more depleted δ13C values, lower concentrations of the fungal biomarker ergosterol and higher concentrations of bacterial PLFA biomarkers and plant wax n-alkane biomarkers than those from maritime Antarctica. Shallow soils (2 cm depth) were wetter, and had higher concentrations of organic matter, ergosterol and bacterial PLFAs, than deeper soils (4 cm and 8 cm depths). Correlative analyses indicated that factors associated with climate change (increased soil moisture, C and organic matter concentrations, and depleted δ13C contents) are likely to give rise to increases in Gram negative bacteria, and decreases in Gram positive bacteria and fungi, in maritime Antarctic soils. Bomb-14C analyses indicated that sub-Antarctic soils at all depths contained significant amounts of modern 14C (C fixed from the atmosphere post c. 1955), whereas modern 14C was restricted to depths of 2 cm and 4 cm in maritime Antarctica. The oldest C (c. 1,745 years BP) was present in the southernmost soil. The higher nitrogen (N) concentrations and δ15N values recorded in the southernmost soil were attributed to N inputs from bird guano. Based on these analyses, we conclude that 5–8 °C rises in air temperature, together with associated increases in precipitation, are likely to have substantial impacts on maritime Antarctic soils, but that, at the rates of climate warming predicted under moderate greenhouse gas emission scenarios, these impacts are likely to take at least a century to manifest themselves.
- Published
- 2020
11. Endemic and cosmopolitan fungal taxa exhibit differential abundances in total and active communities of Antarctic soils
- Author
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Kevin K. Newsham, Clare H. Robinson, and Filipa Cox
- Subjects
0303 health sciences ,030306 microbiology ,Ecology ,Fungi ,Antarctic Regions ,Soil fungi ,15. Life on land ,Biology ,Microbiology ,Soil ,03 medical and health sciences ,Taxon ,Community dynamics ,Abundance (ecology) ,Soil water ,Taxonomic rank ,Species richness ,DNA, Fungal ,Phylogeny ,Soil Microbiology ,Research Articles ,Ecology, Evolution, Behavior and Systematics ,Mycobiome ,Research Article ,030304 developmental biology - Abstract
Summary Our understanding of the diversity and community dynamics of soil fungi has increased greatly through the use of DNA‐based identification. Community characterization of metabolically active communities via RNA sequencing has previously revealed differences between ‘active’ and ‘total’ fungal communities, which may be influenced by the persistence of DNA from nonactive components. However, it is not known how fungal traits influence their prevalence in these contrasting community profiles. In this study, we coextracted DNA and RNA from soil collected from three Antarctic islands to test for differences between total and active soil fungal communities. By matching these geographically isolated fungi against a global dataset of soil fungi, we show that widely dispersed taxa are often more abundant in the total community, whilst taxa restricted to Antarctica are more likely to have higher abundance in the active community. In addition, we find that active communities have lower richness, and show a reduction in the abundance of the most dominant fungi, whilst there are consistent differences in the abundances of certain taxonomic groups between the total and active communities. These results suggest that the views of soil fungal communities offered by DNA‐ and RNA‐based characterization differ in predictable ways.
- Published
- 2019
12. Coming up short: Identifying substrate and geographic biases in fungal sequence databases
- Author
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Maryia Khomich, Håvard Kauserud, Tom Andersen, Filipa Cox, Marie L. Davey, and Carrie Andrew
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0301 basic medicine ,Biome ,Plant Science ,Subtropics ,Biology ,computer.software_genre ,Molecular ecology ,GenBank ,03 medical and health sciences ,UNITE ,Ecosystem ,RDP Bayesian classifier ,Internal transcribed spacer ,Ecology, Evolution, Behavior and Systematics ,Diversity ,Ecology ,Database ,Amazon rainforest ,VDP::Landbruks- og Fiskerifag: 900 ,Ecological Modeling ,Aquatic ecosystem ,Fungi ,ITS region ,Substrate (marine biology) ,030104 developmental biology ,Metabarcoding ,Substrate ,computer ,Mycobiome - Abstract
Insufficient reference database coverage is a widely recognized limitation of molecular ecology ap-proaches which are reliant on database matches for assignment of function or identity. Here, we use datafrom 65 amplicon high-throughput sequencing (HTS) datasets targeting the internal transcribed spacer(ITS) region of fungal rDNA to identify substrates and geographic areas whose underrepresentation in theavailable reference databases could have meaningful impact on our ability to draw ecological conclu-sions. A total of 14 different substrates were investigated. Database representation was particularly poorfor the fungal communities found in aquatic (freshwater and marine) and soil ecosystems. Aquaticecosystems are identified as priority targets for the recovery of novel fungal lineages. A subset of the datarepresenting soil samples with global distribution were used to identify geographic locations andterrestrial biomes with poor database representation. Database coverage was especially poor in tropical,subtropical, and Antarctic latitudes, and the Amazon, Southeast Asia, Australasia, and the Indian sub-continent are identified as priority areas for improving database coverage in fungi. Coming up short: Identifying substrate and geographic biases in fungal sequence databases
- Published
- 2018
13. Environment and host as large-scale controls of ectomycorrhizal fungi
- Author
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Manuel Nicolas, Hyun S. Gweon, Joachim Gehrmann, Walter Seidling, Endla Asi, Lars Vesterdal, Arne Verstraeten, Martin I. Bidartondo, Hans-Peter Dietrich, Pavel Pavlenda, Karin Hansen, Filipa Cox, Sture Wijk, Christopher Carroll, Hans-Werner Schrock, Sue Benham, Laura M. Suz, Yuxin Zhang, Iben Margrete Thomsen, Tine Grebenc, Miklos Manninger, Elena Vanguelova, Paweł Lech, Johannes Eichhorn, Henning Andreae, Päivi Merilä, Frank Jacob, Pasi Rautio, Jan Martin, Bonnie Atkinson, Ferdinand Kristöfel, Peter Waldner, Hugues Titeux, Vít Šrámek, Daniel Žlindra, Nathalie Cools, Marcus Schaub, Bruno De Vos, C. David L. Orme, Henning Meesenburg, Sietse van der Linde, Anne Thimonier, and Natural Environment Research Council (NERC)
- Subjects
0301 basic medicine ,General Science & Technology ,Foraging ,SPECIES-AREA RELATIONSHIP ,Biodiversity ,Geographic Mapping ,SEQUENCE DATA ,Biology ,NITROGEN CRITICAL LOADS ,Forests ,03 medical and health sciences ,FOREST ECOSYSTEMS ,Mycorrhizae ,Forest ecology ,DEPOSITION ,Macroecology ,Soil Microbiology ,Abiotic component ,EUROPEAN FORESTS ,Multidisciplinary ,Science & Technology ,Host Microbial Interactions ,Ecology ,Community structure ,Fungi ,Multidisciplinary Sciences ,Europe ,030104 developmental biology ,MYCORRHIZAL FUNGI ,Guild ,Spatial ecology ,Science & Technology - Other Topics ,FORAGING STRATEGIES ,COMMUNITY STRUCTURE ,human activities ,MICROBIAL DIVERSITY - Abstract
Explaining the large-scale diversity of soil organisms that drive biogeochemical processes—and their responses to environmental change—is critical. However, identifying consistent drivers of belowground diversity and abundance for some soil organisms at large spatial scales remains problematic. Here we investigate a major guild, the ectomycorrhizal fungi, across European forests at a spatial scale and resolution that is—to our knowledge—unprecedented, to explore key biotic and abiotic predictors of ectomycorrhizal diversity and to identify dominant responses and thresholds for change across complex environmental gradients. We show the effect of 38 host, environment, climate and geographical variables on ectomycorrhizal diversity, and define thresholds of community change for key variables. We quantify host specificity and reveal plasticity in functional traits involved in soil foraging across gradients. We conclude that environmental and host factors explain most of the variation in ectomycorrhizal diversity, that the environmental thresholds used as major ecosystem assessment tools need adjustment and that the importance of belowground specificity and plasticity has previously been underappreciated.
- Published
- 2018
14. Multiple environmental factors influence
- Author
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Helena S, Davies, Jeanette, Rosas-Moreno, Filipa, Cox, Paul, Lythgoe, Alastair, Bewsher, Francis R, Livens, Clare H, Robinson, and Jon K, Pittman
- Subjects
Radiation Monitoring ,Mycorrhizae ,Thorium ,Soil Pollutants, Radioactive ,Uranium ,Plants ,Plant Roots ,Radium - Abstract
Ecological consequences of low-dose radioactivity from natural sources or radioactive waste are important to understand but knowledge gaps still remain. In particular, the soil transfer and bioaccumulation of radionuclides into plant roots is poorly studied. Furthermore, better knowledge of arbuscular mycorrhizal (AM) fungi association may help understand the complexities of radionuclide bioaccumulation within the rhizosphere. Plant bioaccumulation of uranium, thorium and radium was demonstrated at two field sites, where plant tissue concentrations reached up to 46.93 μg g
- Published
- 2018
15. Discrete taxa of saprotrophic fungi respire different ages of carbon from Antarctic soils
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Mark H. Garnett, Kevin K. Newsham, Clare H. Robinson, and Filipa Cox
- Subjects
0301 basic medicine ,lcsh:Medicine ,chemistry.chemical_element ,Antarctic Regions ,Fungus ,Biology ,Article ,Fungal Proteins ,03 medical and health sciences ,Soil ,Botany ,lcsh:Science ,Cellulose ,DNA, Fungal ,Soil Microbiology ,Multidisciplinary ,δ13C ,beta-Glucosidase ,lcsh:R ,Radiometric Dating ,Fungi ,Soil chemistry ,Soil carbon ,15. Life on land ,Carbon Dioxide ,biology.organism_classification ,Carbon ,030104 developmental biology ,Helotiales ,chemistry ,Soil water ,lcsh:Q ,Soil microbiology - Abstract
Different organic compounds have distinct residence times in soil and are degraded by specific taxa of saprotrophic fungi. It hence follows that specific fungal taxa should respire carbon of different ages from these compounds to the atmosphere. Here, we test whether this is the case by radiocarbon (14C) dating CO2 evolved from two gamma radiation-sterilised maritime Antarctic soils inoculated with pure single cultures of four fungi. We show that a member of the Helotiales, which accounted for 41–56% of all fungal sequences in the two soils, respired soil carbon that was aged up to 1,200 years BP and which was 350–400 years older than that respired by the other three taxa. Analyses of the enzyme profile of the Helotialean fungus and the fluxes and δ13C values of CO2 that it evolved suggested that its release of old carbon from soil was associated with efficient cellulose decomposition. Our findings support suggestions that increases in the ages of carbon respired from warmed soils may be caused by changes to the abundances or activities of discrete taxa of microbes, and indicate that the loss of old carbon from soils is driven by specific fungal taxa.
- Published
- 2017
16. Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic
- Author
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Filipa, Cox, Kevin K, Newsham, Roland, Bol, Jennifer A J, Dungait, and Clare H, Robinson
- Subjects
Arctic Regions ,ddc:570 ,fungi ,Fungi ,Antarctic Regions ,Ecosystem ,Soil Microbiology ,Demography - Abstract
Antarctica's extreme environment and geographical isolation offers a useful platform for testing the relative roles of environmental selection and dispersal barriers influencing fungal communities. The former process should lead to convergence in community composition with other cold environments, such as those in the Arctic. Alternatively, dispersal limitations should minimise similarity between Antarctica and distant northern landmasses. Using high-throughput sequencing, we show that Antarctica shares significantly more fungi with the Arctic, and more fungi display a bipolar distribution, than would be expected in the absence of environmental filtering. In contrast to temperate and tropical regions, there is relatively little endemism, and a strongly bimodal distribution of range sizes. Increasing southerly latitude is associated with lower endemism and communities increasingly dominated by fungi with widespread ranges. These results suggest that micro-organisms with well-developed dispersal capabilities can inhabit opposite poles of the Earth, and dominate extreme environments over specialised local species.
- Published
- 2016
17. Author Correction: Environment and host as large-scale controls of ectomycorrhizal fungi
- Author
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Johannes Eichhorn, Ferdinand Kristöfel, Joachim Gehrmann, Miklos Manninger, Hugues Titeux, Arne Verstraeten, Bonnie Atkinson, Filipa Cox, Sture Wijk, Christopher Carroll, Paweł Lech, Hyun S. Gweon, Manuel Nicolas, Laura M. Suz, Pavel Pavlenda, Sue Benham, Martin I. Bidartondo, Hans-Peter Dietrich, Yuxin Zhang, Marcus Schaub, Päivi Merilä, Frank Jacob, Lars Vesterdal, Iben Margrete Thomsen, Henning Andreae, Pasi Rautio, Peter Waldner, Walter Seidling, Sietse van der Linde, Daniel Žlindra, Jan Martin, Vít Šrámek, Bruno De Vos, Anne Thimonier, Endla Asi, Hans-Werner Schrock, Elena Vanguelova, Karin Hansen, Tine Grebenc, C. David L. Orme, Henning Meesenburg, and Nathalie Cools
- Subjects
0301 basic medicine ,03 medical and health sciences ,030104 developmental biology ,Multidisciplinary ,Geography ,Fungal ecology ,Scale (music) ,Genealogy - Abstract
Change history: In the HTML version of this Article, author 'Filipa Cox' had no affiliation in the author list, although she was correctly associated with affiliation 3 in the PDF. In addition, the blue circles for 'oak' were missing from Extended Data Fig. 1. These errors have been corrected online.
- Published
- 2018
18. Nitrogen availability is a primary determinant of conifer mycorrhizas across complex environmental gradients
- Author
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Erik A. Lilleskov, Nadia Barsoum, Martin I. Bidartondo, and Filipa Cox
- Subjects
Nutrient ,Environmental change ,Ecology ,Indicator species ,Taiga ,Temperate climate ,Species diversity ,Biology ,Mycorrhiza ,biology.organism_classification ,Ecology, Evolution, Behavior and Systematics ,Ectosymbiosis - Abstract
Global environmental change has serious implications for functional biodiversity in temperate and boreal forests. Trees depend on mycorrhizal fungi for nutrient uptake, but predicted increases in nitrogen availability may alter fungal communities. To address a knowledge gap regarding the effects of nitrogen availability on mycorrhizal communities at large scales, we examine the relationship between nitrogen and ectomycorrhizas in part of a European biomonitoring network of pine forest plots. Our analyses show that increased nitrogen reduces fungal diversity and causes shifts in mycorrhizal community composition across plots, but we do not find strong evidence that within-plot differences in nitrogen availability affect ectomycorrhizal communities. We also carry out exploratory analyses to determine the relative importance of other environmental variables in structuring mycorrhizal communities, and discuss the potential use of indicator species to predict nitrogen-induced shifts in fungal communities.
- Published
- 2010
19. Monitoring ectomycorrhizal fungi at large scales for science, forest management, fungal conservation and environmental policy
- Author
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Louise Hackett, Alan G. Jones, Martin I. Bidartondo, Chris Cheffings, Filipa Cox, Gregory M. Mueller, Sietse van der Linde, David Orme, Sue Benham, Walter Seidling, Laura M. Suz, Nadia Barsoum, Commission of the European Communities, and Natural Environment Research Council (NERC)
- Subjects
Nitrogen deposition ,ICP Forests ,Monitoring ,EXPLORATION TYPES ,[SDV]Life Sciences [q-bio] ,Forest management ,ENGLAND ,Biodiversity ,Air pollution ,DIVERSITY ,Mycorrhizal fungi ,Dominance (ecology) ,IUCN Red List ,Environmental policy ,EUROPEAN FORESTS ,Science & Technology ,NITROGEN DEPOSITION ,Ecology ,Mycorrhizas ,Agroforestry ,AVAILABILITY ,NORWAY SPRUCE ,Forestry ,15. Life on land ,SOIL ,Geography ,Indicator ,13. Climate action ,Guild ,Red list ,0705 Forestry Sciences ,VEGETATION ,COMMUNITIES ,Life Sciences & Biomedicine - Abstract
Key message The ICP Forests network can be a platform for large-scale mycorrhizal studies. Mapping and monitoring of mycorrhizas have untapped potential to inform science, management, conservation and policy regarding distributions, diversity hotspots, dominance and rarity, and indicators of forest changes. Context A dearth of information about fungi at large scales has severely constrained scientific, forest management, fungal conservation and environmental policy efforts worldwide. Nonetheless, fungi fulfil critical functional roles in our changing environments and represent a considerable proportion of terrestrial biodiversity. Mycorrhizal fungi are increasingly viewed as a major functional guild across forest ecosystems, and our ability to study them is expanding rapidly. Aims This study aimed to discuss the potential for starting a mycorrhizal monitoring programme built upon the existing forest monitoring network, raise questions, propose hypotheses and stimulate further discussion. Results An overview of the state-of-the-art regarding forest ectomycorrhizal ecology raises questions and recommendations for scaling up mycorrhizal assessments aimed at informing a variety of stakeholders, with a new focus on conservation and policy. Conclusion Fungal research and conservation are areas that can be informed by ICP Forests and may lead to useful spin-offs; research linked to long-term forest monitoring plots will enhance the relevance of science and conservation.
- Published
- 2014
20. Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi
- Author
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Audrius Menkis, Anna Rosling, Katarina Ihrmark, Karelyn Cruz-Martinez, Gwen-Aëlle Grelet, Timothy Y. James, Filipa Cox, and Björn D. Lindahl
- Subjects
Rhizosphere ,Multidisciplinary ,Ascomycota ,Ecology ,Host (biology) ,Genes, Fungal ,Meristem ,Molecular Sequence Data ,Genes, rRNA ,Biology ,biology.organism_classification ,Taphrinomycotina ,Tracheophyta ,Mycorrhizae ,Botany ,Archaeorhizomycetes ,Ecosystem ,Environmental DNA ,Subphylum ,Phylogeny ,Soil Microbiology - Abstract
Estimates suggest that only one-tenth of the true fungal diversity has been described. Among numerous fungal lineages known only from environmental DNA sequences, Soil Clone Group 1 is the most ubiquitous. These globally distributed fungi may dominate below-ground fungal communities, but their placement in the fungal tree of life has been uncertain. Here, we report cultures of this group and describe the class, Archaeorhizomycetes, phylogenetically placed within subphylum Taphrinomycotina in the Ascomycota. Archaeorhizomycetes comprises hundreds of cryptically reproducing filamentous species that do not form recognizable mycorrhizal structures and have saprotrophic potential, yet are omnipresent in roots and rhizosphere soil and show ecosystem and host root habitat specificity.
- Published
- 2011
21. Nitrogen availability is a primary determinant of conifer mycorrhizas across complex environmental gradients
- Author
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Filipa, Cox, Nadia, Barsoum, Erik A, Lilleskov, and Martin I, Bidartondo
- Subjects
Soil ,Nitrogen ,Mycorrhizae ,Pinus sylvestris ,Biodiversity ,Ecosystem - Abstract
Global environmental change has serious implications for functional biodiversity in temperate and boreal forests. Trees depend on mycorrhizal fungi for nutrient uptake, but predicted increases in nitrogen availability may alter fungal communities. To address a knowledge gap regarding the effects of nitrogen availability on mycorrhizal communities at large scales, we examine the relationship between nitrogen and ectomycorrhizas in part of a European biomonitoring network of pine forest plots. Our analyses show that increased nitrogen reduces fungal diversity and causes shifts in mycorrhizal community composition across plots, but we do not find strong evidence that within-plot differences in nitrogen availability affect ectomycorrhizal communities. We also carry out exploratory analyses to determine the relative importance of other environmental variables in structuring mycorrhizal communities, and discuss the potential use of indicator species to predict nitrogen-induced shifts in fungal communities.
- Published
- 2010
22. Environmental and host filtering of ectomycorrhizal fungi at large scales
- Author
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Sietse van der Linde, Suz, Laura M., David Orme, Filipa Cox, Henning Andreae, Endla Asi, Bonnie Atkinson, Sue Benham, Christopher Carroll, Nathalie Cools, Bruno De Vos, Hans-Peter Dietrich, Johannes Eichhorn, Joachim Gehrmann, Tine Grebenc, Gweon, Hyun S., Karin Hansen, Frank Jacob, Ferdinand Kristöfel, Pawel Lech, Miklos Manninger, Jan Martin, Henning Meesenburg, Päivi Merilä, Manuel Nicolas, Pavel Pavlenda, Pasi Rautio, Marcus Schaub, Hans Werner Schröck, Walter Seidling, Vit Sramek, Anne Thimonier, Iben Margrete Thomsen, Hugues Titeux, Elena Vanguelova, Arne Verstraeten, Vesterdal, L., Peter Waldner, Sture Wijk, Yuxin Zhang, Daniel Zlindra, and Bidartondo, Martin I.
23. A leap forward in geographic scale for forest ectomycorrhizal fungi
- Author
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Filipa Cox, Kath Tubby, Lars Ola Nilsson, Pasi Rautio, Isabella Børja, Erik A. Lilleskov, Lars Vesterdal, Martin I. Bidartondo, and Nadia Barsoum
- Subjects
0106 biological sciences ,ICP Forests ,Resource (biology) ,media_common.quotation_subject ,Forest management ,Climate change ,010603 evolutionary biology ,01 natural sciences ,[SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry ,Environmental monitoring ,Forest ecology ,Function ,Symbiosis ,Function (engineering) ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ,ComputingMilieux_MISCELLANEOUS ,biogeography ,media_common ,function ,Mycorrhizas ,Ecology ,business.industry ,Scale (chemistry) ,Environmental resource management ,Forestry ,mycorrhizas ,15. Life on land ,symbiosis ,Geography ,Biogeography ,13. Climate action ,Spatial ecology ,business ,010606 plant biology & botany - Abstract
The functionally critical role of mycorrhizal fungi in forest ecosystems, and the imminent threat of climate change that may act to alter mycorrhizal functional biodiversity, means there is an urgent need for a regional to continental-scale assessment of mycorrhizal distributions. Until recently, it had not been possible to cost-effectively assess mycorrhizas precisely and accurately. A large-scale survey of ICP Forests plots would be only the first stage in answering many of the questions outlined above, but it is essential if future studies are going to address these questions with hypothesis-driven research in a cohesive manner, rather than remain independent for lack of a unified approach. The chance to utilise the vast network of biomonitoring plots at this time is a remarkable opportunity because it minimises the logistics and costs associated with achieving such an enormous effort and provides a rare stable — past and future — ground for forest ecosystem scientific investigation. In the face of rapid global change, we finally have an opportunity to accurately integrate mycorrhizal distribution data with long-term environmental monitoring, providing a basic understanding of functionally crucial organisms, and at the same time creating an invaluable resource for future research.
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